Question

I am very new to python so please bear with me.

I have a files with atom coordinates. The files look a certain way, but the coordinates are not necessarily on the same line. The file also contains some text, below is a part of the file which is important:

<Gold.Protein.RotatedAtoms>
  28.5571   85.1121    3.9003 C.ar 0  0  0  0  0  0  0  0  0  0  0  0  
  27.3346   84.9085    3.2531 C.ar 0  0  0  0  0  0  0  0  0  0  0  0  
  28.9141   86.4057    4.2554 C.ar 0  0  0  0  0  0  0  0  0  0  0  0
  26.4701   85.9748    2.9810 C.ar 0  0  0  0  0  0  0  0  0  0  0  0 
  28.0456   87.4704    3.9845 C.ar 0  0  0  0  0  0  0  0  0  0  0  0 
  26.8436   87.2569    3.3417 C.ar 0  0  0  0  0  0  0  0  0  0  0  0  
  26.1924   88.0932    3.1196 H   0  0  0  0  0  0  0  0  0  0  0  0   
  27.0510   83.9062    2.9565 H   0  0  0  0  0  0  0  0  0  0  0  0 

what I want to do is the following:
Get the python to recognize if the the number on the 5th row in the 6th column (in our case 3.3417) is more or less than 6. Then, if the value is more than 6 write the FILENAME of the file to a text document. Note that the position of this chunk of information changes in the different files. That is to say, the number 3.3417 is not always on the same row.
Also, all the numbers change all time.

I was thinking that I might loop through the text, scanning for the a line with “Gold.Protein.RotatedAtoms” and then take the 3rd insert on line the line 5 rows down. But how would one do that?

Thanks for your help!

Answer 1

Split all the lines of the text into a list using splitlines().

Find the index of the line with “Gold.Protein.RotatedAtoms” using the enumerate method and a filter in a list comprehension, something like this:

index = [index for index,line in enumerate(all_lines) if "Gold.Protein.RotatedAtoms"  in line]

Add 5 to that index to get the line you need from all_lines, use the split() method to split it into tokens, and finally take out the 3rd element with the index operator (3rd element = line.split()[2]).